findIT_enrichWilcox: findIT_enrichWilcox

In shangguandong1996/FindIT2: find influential TF and Target based on multi-omics data

findIT_enrichWilcox

Description

findIT_enrichWilcox

Usage

findIT_enrichWilcox(
  input_feature_id,
  peak_GR,
  TF_GR_database,
  background_peaks = NULL,
  background_number = 3000
)

Arguments

input_feature_id	a character vector which represent peaks set which you want to find influential TF for
peak_GR	a GRange object represent your whole feature location with a column named feature_id, which your input_feature_id should a part of it.
TF_GR_database	TF peak GRange with a column named TF_id representing you TF name
background_peaks	a character vector which represent background peak set. If you do not assign background peaks, program will sample background_number peaks as background peaks from all feature_id in your peak_GR
background_number	background peaks number

Value

data.frame

Examples

data("test_featureSet")
peak_path <- system.file("extdata", "ATAC.bed.gz", package = "FindIT2")
peak_GR <- loadPeakFile(peak_path)
ChIP_peak_path <- system.file("extdata", "ChIP.bed.gz", package = "FindIT2")
ChIP_peak_GR <- loadPeakFile(ChIP_peak_path)
ChIP_peak_GR$TF_id <- "AT1G28300"

result_findIT_enrichWilcox <- findIT_enrichWilcox(
    input_feature_id = test_featureSet,
    peak_GR = peak_GR,
    TF_GR_database = ChIP_peak_GR
)

shangguandong1996/FindIT2 documentation built on March 1, 2024, 8:34 p.m.